A scientific and accurate understanding of the crisis and threats to water will help to better understand it and consequently proper planning to deal with it. In general, the major contributors to the water threat in the sub-basins of the country are pollution, climate change and drought, population growth, reduction of groundwater levels and desertification. Using gray relational analysis as a multi-criteria decision making method, the country's sub-basins were prioritized based on the severity of the five water threat factors. Since in gray analysis all indices should be quantitative, it is necessary to quantify the respective values for the each index.Then, according to the quantification results, the sub-basins of the country are prioritized by the gray relational analysis method, based on this prioritization of the Namk-lake sub-basin with 0.792 most critical sub-basin in the whole country based on the severity of the five studied threat factors in this paper.It should be noted that the rank is a number between 0 and 1 and the closer one is, the more intense the target. Maharloo and Karakum basins with 0.739 and 0.727 are in the next priorities respectively. Other basins are the Petargan, Dasht-e Kavir, Helle, Jarahi, Karkheh, Gavkhuni, Orumiyeh, Darangir playa, Siah Koh, Mend, Kol, Atrak, Karoon, Hamoun Mashkil, Abrogh-Sirjan, Kavir-e Lut, Hamoun Jazmourian, Marzi-Gharb, South Baluchistan, Aras, Hamoun Hirmand, Gorganroud-Gharehsou, Sefidrud, Bandar-Abbas, Talesh, Hazar, Between Hazar and Sefidrud.